If you're using segger, a quick find-and-replace will take care of that (ditto GCC Makefiles). Must admit that when I started with nrf52 SDK, I too used thge embed-the-application-inside-the-SDK approach. Pretty soon that got cumbersome, so I switched to the softlink approach. The exact approach is to store the SDK somewhere, create a softlink to it in the project directory and have the project files/makefiles use that instead.